Research workbench
Cytochrome C nitrite reductase from wolinella succinogenes with bound substrate nitrite
Analyse Cytochrome C nitrite reductase from wolinella succinogenes with bound substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E80
- Type
- protein
- Length
- 471 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C-552
- EC
- 1.7.2.2
- UniProt
- Q9S1E5
- Ligands
- HEM, YT3, CA, NO2
- Pockets
- 2 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C-552 (EC 1.7.2.2) | protein | 471 | 53% helix, 8% strand | Q9S1E5 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 5 copies · chains A
- YT3 · Yttrium (III) ion · metal · 3 copies · chains A
- CA · Calcium ion · metal · chains A
- NO2 · Nitrite ion · ion · chains A
- ACT · Acetate ion · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.87 | 0.88 | 115 | NO2, YT3, HEM |
| 2 | 51 | 0.65 | 0.95 | 20 | empty |
Modifications
Observed in the structure: 10 cofactor (heme attachment).
Compared structures
- 2E80 · Cytochrome c Nitrite Reductase from Wolinella succinogenes with bound substrate nitrite · the same entry in another collection · chain A against A, TM-score 1.00
- Q9S1E5 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (Q9S1E5) · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9S1E5
- Elsewhere: RCSB PDB 2E80 · PDBe 2E80 · UniProt Q9S1E5
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